Open emilyvansyoc opened 9 months ago
Gian77
commented
9 months ago Hi @emilyvansyoc,
Thanks for using CONSTAX2. At first I would try rerunning using full paths in the command. Also, I think you should add a pathfile.txt and a directory for the training_files.
Please see this https://constax.readthedocs.io/en/latest/tutorial1.html
What do you think @liberjul?
Best,
Gian
emilyvansyoc
commented
9 months ago Hello Gian,
Thanks for your quick reply. I reran adding a pathfile.txt and using full pathways. Here is what I ran:
With that command, I get the same 'cannot find jarfile' error:
$ bash constax.sh /Users/epb5360/miniconda3/envs/constax/bin/constax:87: SyntaxWarning: invalid escape sequence '\ ' if "\ " in pathfile.read(): /Users/epb5360/miniconda3/envs/constax/bin/constax:88: SyntaxWarning: invalid escape sequence ')' raise NameError("Remove any backslashes () from CONSTAXPATH in the pathfile located at: ", args.pathfile) /Users/epb5360/miniconda3/envs/constax/bin/constax:148: SyntaxWarning: invalid escape sequence '\ ' script_loc = script_loc.replace(" ", "\ ") # Add escape characters to paths in case spaces are present /Users/epb5360/miniconda3/envs/constax/bin/constax:162: SyntaxWarning: invalid escape sequence '\ ' if "\ " in pathfile.read(): /Users/epb5360/miniconda3/envs/constax/bin/constax:163: SyntaxWarning: invalid escape sequence ')' raise NameError("Remove any backslashes () from CONSTAXPATH in the pathfile located at: ", new_pathfile) Welcome to CONSTAX version 2.0.20 build 0 - The CONSensus TAXonomy classifier This software is distributed under MIT License © Copyright 2022, Julian A. Liber, Gian M. N. Benucci & Gregory M. Bonito https://github.com/liberjul/CONSTAXv2 https://constax.readthedocs.io/
Please cite us as: CONSTAX2: Improved taxonomic classification of environmental DNA markers Julian Aaron Liber, Gregory Bonito, Gian Maria Niccolò Benucci Bioinformatics, Volume 37, Issue 21, 1 November 2021, Pages 3941–3943; doi: https://doi.org/10.1093/bioinformatics/btab347 Training, with output to /Users/epb5360/scratch/tutorial/training_files/... Using the user-supplied pathfile at /Users/epb5360/scratch/tutorial/pathfile.txt All needed executables exist. SINTAX: RDP: classifier CONSTAX: /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/ python /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//detect_format.py -d /Users/epb5360/scratch/tutorial/sh_general_release_dynamic_s_25.07.2023.fasta 2>&1 UNITE Memory size: 32000mb python /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//FormatRefDB.py -d /Users/epb5360/scratch/tutorial/sh_general_release_dynamic_s_25.07.2023.fasta -t /Users/epb5360/scratch/tutorial/training_files/ -f UNITE -p /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/ Importing subscripts from /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/
Reformatting database
UNITE format detected
Reference database FASTAs formatted in 0.7861969999999999 seconds...
Training Taxonomy
Adding Full LineageDatabase formatting complete
Training SINTAX Classifier -makeudb_usearch /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__UTAX.fasta -output /Users/epb5360/scratch/tutorial/training_files//sintax.db
Training BLAST Classifier makeblastdb -in /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__RDP_trained.fasta -dbtype nucl -out /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__BLAST
Training RDP Classifier java -Xmx -jar classifier train -o /Users/epb5360/scratch/tutorial/training_files//. -s /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__RDP_trained.fasta -t /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__RDP_taxonomy_trained.txt > rdp_train.out 2>&1 Error: Unable to access jarfile classifier cp /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//rRNAClassifier.properties /Users/epb5360/scratch/tutorial/training_files//
Assigning taxonomy to OTU's representative sequences python /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//check_input_names.py -i otus.fasta -sintax formatted_inputs_a5e64b.fasta -db /Users/epb5360/scratch/tutorial/training_files//sintax.db -tabbedout /Users/epb5360/scratch/tutorial/taxonomy_assignments//otu_taxonomy.sintax -strand both -sintax_cutoff 0.8 -threads 10 python /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//split_inputs.py -i formatted_inputs_a5e64b.fasta Input FASTA: formatted_inputs_a5e64b.fasta
/Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0000.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0001.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0002.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0003.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0004.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0005.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0006.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0007.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0008.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0009.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0010.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0011.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0012.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0013.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0014.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0015.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0016.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0017.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0018.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0019.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0020.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0021.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0022.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0023.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0024.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0025.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0026.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0027.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0028.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0029.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0030.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0031.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0032.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0033.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0034.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0035.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0036.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0037.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0038.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0039.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0040.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0041.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0042.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0043.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0044.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0045.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0046.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0047.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0048.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0049.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0050.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0051.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0052.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0053.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0054.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0055.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0056.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0057.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0058.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0059.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0060.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0061.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0062.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0063.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0064.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0065.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0066.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0067.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0068.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0069.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0070.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0071.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0072.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0073.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0074.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0075.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0076.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0077.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0078.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0079.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0080.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0081.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0082.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0083.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0084.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0085.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0086.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0087.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0088.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0089.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out blastn -query formatted_inputs_a5e64b_0090.fasta -db /Users/epb5360/scratch/tutorial/training_files// -num_threads 10 -outfmt 7 qacc sacc evalue bitscore pident qcovs -max_target_seqs 10 >> /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out python /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//blast_to_df.py -i /Users/epb5360/scratch/tutorial/taxonomy_assignments//blast.out -o /Users/epb5360/scratch/tutorial/taxonomy_assignments//otu_taxonomy.blast -d /Users/epb5360/scratch/tutorial/sh_general_release_dynamic_s_25.07.2023.fasta -t /Users/epb5360/scratch/tutorial/training_files/ -f UNITE java -Xmx -jar classifier classify --conf 0.8 --format allrank --train_propfile /Users/epb5360/scratch/tutorial/training_files//rRNAClassifier.properties -o /Users/epb5360/scratch/tutorial/taxonomy_assignments//otu_taxonomy.rdp formatted_inputs_a5e64b.fasta
Combining Taxonomies python /Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//CombineTaxonomy.py -c 0.8 -o /Users/epb5360/scratch/tutorial/taxonomy_assignments// -x /Users/epb5360/scratch/tutorial/taxonomy_assignments// -b -e 1.0 -m 10 -p 0.0 -f UNITE -d /Users/epb5360/scratch/tutorial/sh_general_release_dynamic_s_25.07.2023.fasta -t /Users/epb5360/scratch/tutorial/training_files/ -i False --hl null --iso_qc 75 --iso_id 1 --hl_qc 75 --hl_id 1 -s false -n false --make_plot has been deprecated in v2.0.18. The script ComparisonBars.R is available if you wish to plot the sumary statistics.
And, a similar error in one of the logfiles:
$ cat log_constax2_2023-12-14_12-24-38.txt
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 261: : command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 272: makeblastdb: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 347: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 360: : command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/constax_no_inputs.sh: line 383: blastn: command not found
Error: Unable to access jarfile classifier
Traceback (most recent call last):
File "/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0//CombineTaxonomy.py", line 16, in
The files located in the 'taxonomy_assignments' folder are empty. It seems like it still cannot access part of the scripts? Here is the pathfile below. I left out the usearch path since I'd like to use the vsearch install.
CONSTAXPATH=/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/ RDPPATH=classifier
Gian77
commented
9 months ago Hi @emilyvansyoc,
Please try without the ~/ in the PATH, just use the full PATHs.\ Also, what's in your pathfile.txt?
Best,
Gian
emilyvansyoc
commented
9 months ago Hello, Sorry, I get the same error when using full path names. Here is the content of the pathfile.txt: $ cat pathfile.txt CONSTAXPATH=/Users/epb5360/miniconda3/pkgs/constax-2.0.20-pyhdfd78af_0/opt/constax-2.0.20-0/
liberjul
commented
9 months ago Hi @emilyvansyoc ,
Thanks for bringing this issues forward, and I'll do my best to get CONSTAX fixed shortly. Some questions which could help:
python -V) I suspect that the warnings are new in python 3.12 and I will need to edit the scripts to prevent them (see this article). However, this won't break the current functionality.blastn and makeblastdb? If so, you should add the directory with --blast_path java -Xmx -jar classifier train? If so, you should add the path of classifier.jar with --rdp_path ?I hope those help,
Julian
emilyvansyoc
commented
9 months ago Hi Julian,
Thanks so much for continuing to troubleshoot this with me. Yes, I'm running python 3.12.
The path to which classifier (/Users/epb5360/miniconda3/envs/constax/bin/classifier) is symlinked to /Users/epb5360/miniconda3/envs/constax/share/rdptools-2.0.3-1/classifier.jar. Adding the full path to --rdp_path seems to fix the 'classifier not found' error.
--blast_path doesn't seem to be an accepted argument to the contax command. I can run blastn and makeblastdb in the conda environment with no problems. Since these are separate paths, they may have to have separate path arguments?
After changing the classifier pathway, this is now running the train step and erroring out on memory (I'm maxed out on my M2 Max at ~60GB), so I'll get this up and running on the cluster and get back to you on success rates! It is giving this error for the blast pathway:
Reformatting database
UNITE format detected
Reference database FASTAs formatted in 0.7850509999999999 seconds...
Training Taxonomy
Duplicate taxa being handled with numerical suffices
Adding Full LineageDatabase formatting complete
java -Xmx -jar /Users/epb5360/miniconda3/envs/constax/share/rdptools-2.0.3-1/classifier.jar train -o /Users/epb5360/scratch/tutorial/training_files//. -s /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__RDP_trained.fasta -t /Users/epb5360/scratch/tutorial/training_files//sh_general_release_dynamic_s_25.07.2023__RDP_taxonomy_trained.txt > rdp_train.out 2>&1
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at edu.msu.cme.rdp.classifier.train.TreeFactory.createGenusWordConditionalProb(TreeFactory.java:345)
at edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker.
emrog13
commented
8 months ago Hello,
Thinking I'm experiencing a similar issue where blast doesn't seem to be working in CONSTAX even though the blastn and makeblastdb commands are working in my conda environment, and the commands are located in the bin directory of the environment. In the outputs, both the blast database training files and blast taxonomy files are empty, then when the taxonomy is being combined the main output is also empty.
I found early in the slurm files when it's checking the program pathfiles, where the output says BLAST is not executable which I believe aligns with the constax.sh line 368 or constax_no_inputs.sh line 216? Don't know if that helps find the issue with blast.
Emily
liberjul
commented
8 months ago Hi @emrog13 ,
I've been trying to figure out this issue and will need to have a more permanent solution. However, a temporary fix if you are on a cluster is to 1) find the location of constax_no_inputs.sh (should be symbolically linked to same location printed by which constax), 2) edit it somewhere outside an if statement, such as line 16, to include module load blast, or something equivalent.
I'll do my best to include a proper solution in the next version.
Best,
Julian
emrog13
commented
8 months ago Thanks Julian! Hope it's not too difficult to fix and can let you know if I find anything that could be helpful!
Emily
emilyvansyoc
commented
8 months ago Hello,
I wanted to follow up on this since I'm desperately hoping I can get CONSTAX2 working to solve some issues with a very tricky ITS2 dataset that I am working on!
I ran this on a cluster and can report back some key issues, a few temporary fixes, and the (seemingly) last dependency issue.
I re-installed in a conda environment with python 3.6 which solves the syntax warnings.
Finding the CONSTAXPATH and path to the RDP classifier (NOT the symlinked path) fixed those issues. Adding module load blast into the contax_no_inputs.sh script at line 16 solved the missing BLAST dependency.
Now, I am getting errors in the CONSTAX log that the sintax commands are not found, suggesting that CONSTAX can't find the VSEARCH executable, even though which vsearch is successful. Adding --sintax_path /path-to/conda_envs/constax/bin/vsearch to the constax.sh commands is not sufficient. It seems that adding "SINTAXPATH=/path-to/conda_env/constax/bin/vsearch" DOES work - I'll report back once that runs through on the cluster.
Perhaps the main issue here is that constax is having trouble finding dependencies on a standard conda install, since these issues replicated on an Apple silicon and a cluster Linux Redhat environment. Hopefully that's relatively easy to fix!
emilyvansyoc
commented
8 months ago Good news! This is now up and running with the fixes mentioned above. --sintax_path was not recognized as a command. The training_files and taxonomy_output directories contain the same files as listed in the documentation (with the exception of 'consensus_taxonomy.txt` located in the taxonomy_output directory -is that because I don't have isolates?)
Here is a summary of what I tweaked to get this running on an institutional cluster in a Linux environment. Hopefully this will help others who have the same dependency issues:
conda create -n constax python=3.6 -> conda install constax). module load blast somewhere around line 16 (note that this won't work on a local install, and won't work if your institutional cluster does not have a BLAST module) --rdp_path in the constax commands Then, the final constax commands look like this (for training):
constax \ --num_threads $THREADS \ --mem $MEM \ --db $DB \ --input myotus.fasta \ --trainfile /path/to/training \ --train \ --tax /path/to/taxoutput \ --output /path/to/output \ --conf 0.8 \ --blast \ --pathfile /path/to/pathfile.txt \ --rdp_path /path/to/rdp
I hope this is helpful, and thank you for writing this software! In my own dataset, I get fairly divergent results when using an RDP classifier versus sintax, so this seems like the best option to have an empirical way to choose which taxonomic assignment is best supported.
Gian77
commented
8 months ago I am glad it is running @emilyvansyoc, and thanks for using CONSTAX2! Please let us know if you have any other issues. Best, Gian
Hello, I just downloaded and installed CONSTAX into a new conda environment. It seems there are some out-of-the-bag dependency issues (or incomplete installation, perhaps?) and a weird syntax warning that I'm assuming may be a bug or typo. I am using CONSTAX version 2.0.20 build 0 on an apple M2 Max.
FIRST: When running "constax" or any constax commands, these syntax warnings show before any stdout: $ constax /Users/epb5360/miniconda3/envs/constax/bin/constax:87: SyntaxWarning: invalid escape sequence '\ ' if "\ " in pathfile.read(): /Users/epb5360/miniconda3/envs/constax/bin/constax:88: SyntaxWarning: invalid escape sequence ')' raise NameError("Remove any backslashes () from CONSTAXPATH in the pathfile located at: ", args.pathfile) /Users/epb5360/miniconda3/envs/constax/bin/constax:148: SyntaxWarning: invalid escape sequence '\ ' script_loc = script_loc.replace(" ", "\ ") # Add escape characters to paths in case spaces are present /Users/epb5360/miniconda3/envs/constax/bin/constax:162: SyntaxWarning: invalid escape sequence '\ ' if "\ " in pathfile.read(): /Users/epb5360/miniconda3/envs/constax/bin/constax:163: SyntaxWarning: invalid escape sequence ')' raise NameError("Remove any backslashes () from CONSTAXPATH in the pathfile located at: ", new_pathfile) Welcome to CONSTAX version 2.0.20 build 0 - The CONSensus TAXonomy classifier This software is distributed under MIT License © Copyright 2022, Julian A. Liber, Gian M. N. Benucci & Gregory M. Bonito https://github.com/liberjul/CONSTAXv2 https://constax.readthedocs.io/
Please cite us as: CONSTAX2: Improved taxonomic classification of environmental DNA markers Julian Aaron Liber, Gregory Bonito, Gian Maria Niccolò Benucci Bioinformatics, Volume 37, Issue 21, 1 November 2021, Pages 3941–3943; doi: https://doi.org/10.1093/bioinformatics/btab347 Input file otus.fasta does not exist, exiting... Command 'bash -c '/Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh'' returned non-zero exit status 1.
SECOND:
I ran the training command,
constax --num_threads 10 --mem 32000 --db /path/to/sh_general_release_dynamic_s_25.07.2023.fasta --train --output . --make_plotand got the following errors in stdout. Note that runningwhich vsearchreturns/Users/epb5360/miniconda3/envs/constax/bin/vsearchlocated in the conda environment where it should be.STDOUT: $ constax --num_threads 10 --mem 32000 --db ~/bioinformatics/refs/unite-alleuks/sh_general_release_dynamic_s_25.07.2023.fasta --train --input ~/vsearch-ITS/otus.fasta --output . --make_plot
/Users/epb5360/miniconda3/envs/constax/bin/constax:87: SyntaxWarning: invalid escape sequence '\ ' if "\ " in pathfile.read(): /Users/epb5360/miniconda3/envs/constax/bin/constax:88: SyntaxWarning: invalid escape sequence ')' raise NameError("Remove any backslashes () from CONSTAXPATH in the pathfile located at: ", args.pathfile) /Users/epb5360/miniconda3/envs/constax/bin/constax:148: SyntaxWarning: invalid escape sequence '\ ' script_loc = script_loc.replace(" ", "\ ") # Add escape characters to paths in case spaces are present /Users/epb5360/miniconda3/envs/constax/bin/constax:162: SyntaxWarning: invalid escape sequence '\ ' if "\ " in pathfile.read(): /Users/epb5360/miniconda3/envs/constax/bin/constax:163: SyntaxWarning: invalid escape sequence ')' raise NameError("Remove any backslashes () from CONSTAXPATH in the pathfile located at: ", new_pathfile) Welcome to CONSTAX version 2.0.20 build 0 - The CONSensus TAXonomy classifier This software is distributed under MIT License © Copyright 2022, Julian A. Liber, Gian M. N. Benucci & Gregory M. Bonito https://github.com/liberjul/CONSTAXv2 https://constax.readthedocs.io/
Please cite us as: CONSTAX2: Improved taxonomic classification of environmental DNA markers Julian Aaron Liber, Gregory Bonito, Gian Maria Niccolò Benucci Bioinformatics, Volume 37, Issue 21, 1 November 2021, Pages 3941–3943; doi: https://doi.org/10.1093/bioinformatics/btab347 Overwriting previous classification... Training, with output to ./training_files... Using the user-supplied pathfile at /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/pathfile.txt All needed executables exist. SINTAX: vsearch RDP: classifier CONSTAX: /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0 python /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/detect_format.py -d /Users/epb5360/bioinformatics/refs/unite-alleuks/sh_general_release_dynamic_s_25.07.2023.fasta 2>&1 UNITE Memory size: 32000mb python /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/FormatRefDB.py -d /Users/epb5360/bioinformatics/refs/unite-alleuks/sh_general_release_dynamic_s_25.07.2023.fasta -t ./training_files -f UNITE -p /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0 Importing subscripts from /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0
Reformatting database
UNITE format detected
Reference database FASTAs formatted in 0.773174 seconds...
Database formatting complete
Training SINTAX Classifier vsearch -makeudb_usearch ./training_files/sh_general_release_dynamic_s_25.07.2023__UTAX.fasta -output ./training_files/sintax.db
Training UTAX Classifier -utax_train ./training_files/sh_general_release_dynamic_s_25.07.2023__UTAX.fasta -report ./training_files/utax_db_report.txt -taxconfsout ./training_files/utax.tc -utax_splitlevels NVpcofgs -utax_trainlevels kpcofgs -log ./training_files/utax_train.log -report ./training_files/utax_report.txt -makeudb_utax ./training_files/sh_general_release_dynamic_s_25.07.2023__UTAX.fasta -taxconfsin ./training_files/utax.tc -output ./training_files/utax.db -log ./training_files/make_udb.log -report ./training_files/utax_report.txt
Training RDP Classifier java -Xmx -jar classifier train -o ./training_files/. -s ./training_files/sh_general_release_dynamic_s_25.07.2023__RDP_trained.fasta -t ./training_files/sh_general_release_dynamic_s_25.07.2023__RDP_taxonomy_trained.txt > rdp_train.out 2>&1 Error: Unable to access jarfile classifier cp /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/rRNAClassifier.properties ./training_files/
Assigning taxonomy to OTU's representative sequences python /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/check_input_names.py -i /Users/epb5360/bioinformatics/gomez-hominid/vsearch-ITS/otus.fasta vsearch -sintax formatted_inputs_230d1d.fasta -db ./training_files/sintax.db -tabbedout ./taxonomy_assignments/otu_taxonomy.sintax -strand both -sintax_cutoff 0.8 -threads 10 sed -i'' -e 's|([0-1][.][0-9]{2}|&00|g' ./taxonomy_assignments/otu_taxonomy.sintax -utax formatted_inputs_230d1d.fasta -db ./training_files/utax.db -strand both -utaxout ./taxonomy_assignments/otu_taxonomy.utax -utax_cutoff 0.8 -threads 10 java -Xmx -jar classifier classify --conf 0.8 --format allrank --train_propfile ./training_files/rRNAClassifier.properties -o ./taxonomy_assignments/otu_taxonomy.rdp formatted_inputs_230d1d.fasta
Combining Taxonomies python /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/CombineTaxonomy.py -c 0.8 -o ./ -x ./taxonomy_assignments/ -f UNITE -d /Users/epb5360/bioinformatics/refs/unite-alleuks/sh_general_release_dynamic_s_25.07.2023.fasta -t ./training_files -i False --hl null --iso_qc 75 --iso_id 1 --hl_qc 75 --hl_id 1 -s false -n false --make_plot has been deprecated in v2.0.18. The script ComparisonBars.R is available if you wish to plot the sumary statistics. (constax)
Then, it creates several log files, two of which are empty.
The file "log_constax2_2023-12-14_09-41-18.txt" has this: $ cat log_constax2_2023-12-14_09-41-18.txt /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh: line 219: [: -gt: unary operator expected /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh: line 261: vsearch: command not found /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh: line 277: : command not found /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh: line 281: : command not found /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh: line 360: vsearch: command not found sed: ./taxonomy_assignments/otu_taxonomy.sintax: No such file or directory /Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/constax_no_inputs.sh: line 391: : command not found Error: Unable to access jarfile classifier Traceback (most recent call last): File "/Users/epb5360/miniconda3/envs/constax/opt/constax-2.0.20-0/CombineTaxonomy.py", line 16, in
import pandas as pd
ModuleNotFoundError: No module named 'pandas'
Hopefully this is an easy fix or a typo in my code! Thanks for creating this tool, I am hopeful that it will increase the current ~50% of taxonomically assigned OTUs using the dada2 tax classifier. -Emily